Certain Chemical Entities, Compositions, and Methods

Chemical entities that modulate smooth muscle myosin and/or non-muscle myosin, pharmaceutical compositions and methods of treatment of diseases and conditions associated with smooth muscle myosin and/or non-muscle myosin are described.

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Description

This application claims the benefit of U.S. Patent Application No. 61/026,428, filed Feb. 5, 2008, which is hereby incorporated by reference.

Provided are certain chemical entities that modulate smooth muscle myosin and/or non-muscle myosin, pharmaceutical compositions and methods of treatment of diseases and conditions associated with smooth muscle myosin and/or non-muscle myosin.

Myosin is present in all muscle and non-muscle cells. Of the ten distinct classes of myosin in human cells, myosin-II is thought to be the form responsible for contraction of skeletal, cardiac, and smooth muscle. Myosin-II is also the isoform present in non-muscle myosins, also known as cytoplasmic myosins. The non-muscle myosins are ubiquitously present in eukaryotic cells, where the smooth muscle myosins are generally present in smooth muscle cells.

Myosin-II is significantly different in amino acid composition and in overall structure from myosins in the other nine distinct classes. Myosin-II consists of two globular head domains, called Subfragment-1 or S1, linked together by a long alpha-helical coiled-coiled tail. Proteolysis of myosin generates either S1 or heavy meromyosin (HMM, a two-headed form with a truncated tail), depending on the proteolysis conditions. S1 contains the ATPase and actin-binding properties of the molecule. S1 has been shown to be sufficient to move actin filaments in vitro, and is therefore likely to be the motor domain of the molecule.

Although myosin-II isoforms from various tissues differ in a number of biological properties, they share the same basic molecular structure as a dimer of two heavy chains (approximately 200 kDa) which are noncovalently associated with two pairs of light chains (approximately 20 and 17 kDa). The two globular amino-terminal heads are tethered together by the carboxy-terminal alpha-helical coiled-coil that forms a tail. The tails are believed to be involved in the assembly of myosin molecules into filaments, whereas the heads are thought to have an actin-activated Mg2+-ATPase activity. Each myosin head can be divided by three protease-sensitive regions into peptides of approximately 25, 50, and 20 kDa. The more amino-terminal 25 kDa-50 kDa junction is close to the ATP binding region, whereas the actin-binding domain is near the 50 kDa-20 kDa junction.

S1 consists of a globular actin binding and nucleotide binding region known as the catalytic domain. This domain is attached at its carboxy-terminus to an alpha-helix that has two light chains of about 20 kDa each wrapped around it. This light-chain binding domain of S1 is known as the lever arm. Upon transitioning from the pre-stroke to the post-stroke state, the lever arm is believed to swing through an angle of about 90 degrees about a fulcrum point in the catalytic domain near the nucleotide-binding site. The “power stroke” is driven by the hydrolysis of ATP.

The other end of the myosin molecule is an alpha-helical coiled-coiled tail involved in self assembly of myosin molecules into bipolar thick filaments. These thick filaments interdigitate between thinner actin filaments, and the two filament systems slide past one another during contraction of the muscle. This filament sliding mechanism is thought to involve conformational changes in the myosin heads causing them to walk along the thin actin filaments at the expense of ATP hydrolysis. While non-muscle myosins act in a similar manner, they are understood to slide at a slower velocity than the smooth muscle myosins.

The complete cDNA of the human smooth muscle myosin has been described. The sequence of human smooth muscle myosin is 52% identical to human cardiac myosin in the catalytic S1 region. See, for example, PCT publication No. WO 03/14323.

Provided is at least one chemical entity chosen from compounds of Formula I

and pharmaceutically acceptable salts thereof wherein

R1 is selected from hydrogen and optionally substituted alkyl; cyano, halo, azido, optionally substituted amino, optionally substituted alkoxy, optionally substituted aryloxy, optionally substituted alkoxycarbonyl, optionally substituted aminocarbonyl, optionally substituted aminosulfonyl, sulfonyl, sulfinyl, and sulfanyl;

Z1 is selected from optionally substituted aryl, optionally substituted heteroaryl, optionally substituted cycloalkyl, and optionally substituted heterocycloalkyl, cyano, optionally substituted alkyl, optionally substituted acyl, optionally substituted alkoxycarbonyl, optionally substituted amino, optionally substituted aminocarbonyl, optionally substituted aminosulfonyl, optionally substituted carbamimidoyl, optionally substituted alkoxy, optionally substituted aryloxy, optionally substituted heteroaryloxy, optionally substituted heterocycloalkyloxy, optionally substituted alkenyl, optionally substituted alkynyl, sulfonyl, sulfinyl, and sulfanyl;

Z2 is selected from optionally substituted amidino, carboxyl, optionally substituted alkoxy carbonyl, optionally substituted acyl, optionally substituted alkenyl, optionally substituted alkyl, optionally substituted heterocycloalkyl, optionally substituted heteroaryl, and optionally substituted aminocarbonyl;

Z3 is chosen from hydrogen and optionally substituted alkyl; and

R3 is chosen from hydrogen and optionally substituted alkyl.

Also provided is a pharmaceutically acceptable composition comprising a pharmaceutically acceptable carrier and at least one chemical entity described herein.

Also provided is a packaged pharmaceutical composition comprising a pharmaceutical composition described herein and instructions for using the composition to treat a patient suffering from a disease associated with smooth muscle myosin or non-muscle myosin.

Also provided is a method of treating or ameliorating a disease associated with smooth muscle myosin or non-muscle myosin in a mammal which method comprises administering to a mammal in need thereof a therapeutically effective amount of at least one chemical entity described herein.

Other aspects and embodiments will be apparent to those skilled in the art from the following detailed description.

As used herein, the following words and phrases are generally intended to have the meanings as set forth below, except to the extent that the context in which they are used indicates otherwise.

The following abbreviations and terms have the indicated meanings throughout:

  • ADP=adenosine 5′-diphosphate
  • ATP=adenosine 5′-triphosphate
  • Boc=tert-butoxycarbonyl
  • BSA=bovine serum albumin
  • c-=cyclo
  • DCM dichloromethane=methylene chloride=CH2Cl2
  • DIEA=DIPEA=N,N-diisopropylethylamine
  • DMF=N,N-dimethylformamide
  • (DPPF)PdCl2=[1,1′-bis(diphenylphosphino)ferrocene]dichloropalladium(II)
  • DTT=DL-dithiothreitol
  • EGTA=ethylene glycol tetraacetic acid
  • EtOAc=ethyl acetate
  • EtOH=ethanol
  • g=gram
  • h or hr=hour
  • HBTU=O(benzotriazol-1-yl)-N,N,N′,N′-tetramethyluronium hexafluorophosphate
  • HOBt=1-hydroxybenzotriazole
  • HPLC=high pressure liquid chromatography
  • i-=iso
  • kg or Kg=kilogram
  • L or I=liter
  • LC/MS=LCMS=liquid chromatography-mass spectrometry
  • LRMS=low resolution mass spectrometry
  • m/z=mass-to-charge ratio
  • Me=methyl
  • min=minute
  • mL=milliliter
  • □L=microliter
  • n-=normal
  • NADH=nicotinamide adenine dinucleotide
  • PEP=phosphoenolpyruvic acid
  • Ph=phenyl
  • Pd(Ph)4=tetrakis(triphenylphosphine)palladium (0)
  • psi=pressure in pound square inch gauge
  • PIPES=1,4-piperazinediethanesulfonic acid
  • RB=round bottom
  • RP-HPLC=reverse phase-high pressure liquid chromatography
  • rt or RT=room temperature
  • s-=sec-=secondary
  • t-=tert-=tertiary
  • THF=tetrahydrofuran

As used herein, when any variable occurs more than one time in a chemical formula, its definition on each occurrence is independent of its definition at every other occurrence.

As used herein, a dash (“−”) that is not between two letters or symbols is used to indicate a point of attachment for a substituent. For example, —CONH2 is attached through the carbon atom.

As used herein, “optional” or “optionally” is meant that the subsequently described event or circumstance may or may not occur, and that the description includes instances where the event or circumstance occurs and instances in which it does not. For example, “optionally substituted alkyl” encompasses both “alkyl” and “substituted alkyl” as defined below. It will be understood by those skilled in the art, with respect to any group containing one or more substituents, that such groups are not intended to introduce any substitution or substitution patterns that are sterically impractical, synthetically non-feasible and/or inherently unstable.

As used herein, the term “ATPase” refers to an enzyme that is capable of hydrolyzing ATP. ATPases include proteins comprising molecular motors such as myosins.

As used herein, “alkyl” refers to straight chain and branched chain having the indicated number of carbon atoms, usually from 1 to 20 carbon atoms, for example 1 to 8 carbon atoms, such as 1 to 6 carbon atoms. For example C1-C6 alkyl encompasses both straight and branched chain alkyl of from 1 to 6 carbon atoms. When an alkyl residue having a specific number of carbons is named, all branched and straight chain versions having that number of carbons are intended to be encompassed; thus, for example, “butyl” is meant to include n-butyl, sec-butyl, isobutyl and t-butyl; “propyl” includes n-propyl and isopropyl. “Lower alkyl” refers to alkyl groups having one to six carbons. Examples of alkyl groups include methyl, ethyl, propyl, isopropyl, n-butyl, sec-butyl, tert-butyl, pentyl, 2-pentyl, isopentyl, neopentyl, hexyl, 2-hexyl, 3-hexyl, 3-methylpentyl, and the like. Alkylene is a subset of alkyl, referring to the same residues as alkyl, but having two points of attachment. Alkylene groups will usually have from 2 to 20 carbon atoms, for example 2 to 8 carbon atoms, such as from 2 to 6 carbon atoms. For example, C0 alkylene indicates a covalent bond and C1 alkylene is a methylene group.

As used herein, “alkenyl” refers to an unsaturated branched or straight-chain alkyl group having at least one carbon-carbon double bond derived by the removal of one molecule of hydrogen from adjacent carbon atoms of the parent alkyl. The group may be in either the cis or trans configuration about the double bond(s). Typical alkenyl groups include, but are not limited to, ethenyl; propenyls such as prop-1-en-1-yl, prop-1-en-2-yl, prop-2-en-1-yl (allyl), prop-2-en-2-yl; butenyls such as but-1-en-1-yl, but-1-en-2-yl, 2-methyl-prop-1-en-1-yl, but-2-en-1-yl, but-2-en-1-yl, but-2-en-2-yl, buta-1,3-dien-1-yl, buta-1,3-dien-2-yl; and the like. In certain embodiments, an alkenyl group has from 2 to 20 carbon atoms and in other embodiments, from 2 to 6 carbon atoms. “Lower alkenyl” refers to alkenyl groups having two to six carbons.

As used herein, “alkynyl” refers to an unsaturated branched or straight-chain alkyl group having at least one carbon-carbon triple bond derived by the removal of two molecules of hydrogen from adjacent carbon atoms of the parent alkyl. Typical alkynyl groups include, but are not limited to, ethynyl; propynyls such as prop-1-yn-1-yl, prop-2-yn-1-yl; butynyls such as but-1-yn-1-yl, but-1-yn-3-yl, but-3-yn-1-yl; and the like. In certain embodiments, an alkynyl group has from 2 to 20 carbon atoms and in other embodiments, from 3 to 6 carbon atoms. “Lower alkynyl” refers to alkynyl groups having two to six carbons.

As used herein, “cycloalkyl” refers to a non-aromatic carbocyclic ring, usually having from 3 to 7 ring carbon atoms. The ring may be saturated or have one or more carbon-carbon double bonds. Examples of cycloalkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, cyclopentenyl, cyclohexyl, and cyclohexenyl, as well as bridged and caged ring groups such as norbornane.

As used herein, “alkoxy” refers to an alkyl group of the indicated number of carbon atoms attached through an oxygen bridge such as, for example, methoxy, ethoxy, propoxy, isopropoxy, n-butoxy, sec-butoxy, tert-butoxy, pentyloxy, 2-pentyloxy, isopentyloxy, neopentyloxy, hexyloxy, 2-hexyloxy, 3-hexyloxy, 3-methylpentyloxy, and the like. Alkoxy groups will usually have from 1 to 7 carbon atoms attached through the oxygen bridge. “Lower alkoxy” refers to alkoxy groups having one to six carbons.

As used herein, “mono- and di-alkylcarboxamide” refers to a group of the formula —(C═O)NRaRb where Ra and Rb are independently chosen from hydrogen and alkyl groups of the indicated number of carbon atoms, provided that Ra and Rb are not both hydrogen.

As used herein, “acyl” refers to the groups H—C(O)—; (alkyl)-C(O)—; (cycloalkyl)-C(O)—; (aryl)-C(O)—; (heteroaryl)-C(O)—; and (heterocycloalkyl)-C(O)—, wherein the group is attached to the parent structure through the carbonyl functionality and wherein alkyl, cycloalkyl, aryl, heteroaryl, and heterocycloalkyl are as described herein. Acyl groups have the indicated number of carbon atoms, with the carbon of the keto group being included in the numbered carbon atoms. For example a C2 acyl group is an acetyl group having the formula CH3(C═O)—.

As used herein, “formyl” refers to the group —C(O)H.

As used herein, “carboxy” and/or “carboxyl” refer to the group —C(O)OH.

As used herein, “alkoxycarbonyl” refers to a group of the formula (alkoxy)(C═O)— attached through the carbonyl carbon wherein the alkoxy group has the indicated number of carbon atoms. Thus a C1-C6 alkoxycarbonyl group is an alkoxy group having from 1 to 6 carbon atoms attached through its oxygen to a carbonyl linker.

As used herein, “azido” refers to the group —N3.

As used herein, “amino” refers to the group —NH2.

As used herein, “mono- and di-(alkyl)amino” refers to secondary and tertiary alkyl amino groups, wherein the alkyl groups are as defined above and have the indicated number of carbon atoms. The point of attachment of the alkylamino group is on the nitrogen. Examples of mono- and di-alkylamino groups include ethylamino, dimethylamino, and methyl-propyl-amino.

As used herein, “aminocarbonyl” refers to the group —CONRbRc, where

Rb is chosen from H, optionally substituted C1-C6 alkyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, and optionally substituted heteroaryl, optionally substituted alkoxy; and

Rc is chosen from hydrogen and optionally substituted C1-C4 alkyl; or

Rb and Rc taken together with the nitrogen to which they are bound, form an optionally substituted 5- to 7-membered nitrogen-containing heterocycloalkyl which optionally includes 1 or 2 additional heteroatoms chosen from O, N, and S in the heterocycloalkyl ring;

where each substituted group is independently substituted with one or more substituents independently chosen from C1-C4 alkyl, aryl, heteroaryl, aryl-C1-C4 alkyl-, heteroaryl-C1-C4 alkyl-, C1-C4 haloalkyl, —OC1-C4 alkyl, —OC1-C4 alkylphenyl, —C1-C4 alkyl-OH, —OC1-C4 haloalkyl, halo, —OH, —NH2, —C1-C4 alkyl-NH2, —N(C1-C4 alkyl)(C1-C4 alkyl), —NH(C1-C4 alkyl), —N(C1-C4 alkyl)(C1-C4 alkylphenyl), —NH(C1-C4 alkylphenyl), cyano, nitro, oxo (as a substituent for cycloalkyl, heterocycloalkyl, or heteroaryl), —CO2H, —C(O)OC1-C4 alkyl, —CON(C1-C4 alkyl)(C1-C4 alkyl), —CONH(C1-C4 alkyl), —CONH2, —NHC(O)(C1-C4 alkyl), —NHC(O)(phenyl), —N(C1-C4 alkyl)C(O)(C1-C4 alkyl), —N(C1-C4 alkyl)C(O)(phenyl), —C(O)C1-C4 alkyl, —C(O)C1-C4 alkylphenyl, —C(O)C1-C4 haloalkyl, —OC(O)C1-C4 alkyl, —SO2(C1-C4 alkyl), —SO2(phenyl), —SO2(C1-C4 haloalkyl), —SO2NH2, —SO2NH(C1-C4 alkyl), —SO2NH(phenyl), —NHSO2(C1-C4 alkyl), —NHSO2(phenyl), and —NHSO2(C1-C4 haloalkyl).

As used herein, “aryl” refers to: 6-membered carbocyclic aromatic rings, for example, benzene; bicyclic ring systems wherein at least one ring is carbocyclic and aromatic, for example, naphthalene, indane, and tetralin; and tricyclic ring systems wherein at least one ring is carbocyclic and aromatic, for example, fluorene.

For example, aryl includes 6-membered carbocyclic aromatic rings fused to a 5- to 7-membered heterocycloalkyl ring containing 1 or more heteroatoms chosen from N, O, and S. For such fused, bicyclic ring systems wherein only one of the rings is a carbocyclic aromatic ring, the point of attachment may be at the carbocyclic aromatic ring or the heterocycloalkyl ring. Bivalent radicals formed from substituted benzene derivatives and having the free valences at ring atoms are named as substituted phenylene radicals. Bivalent radicals derived from univalent polycyclic hydrocarbon radicals whose names end in “-yl” by removal of one hydrogen atom from the carbon atom with the free valence are named by adding “-idene” to the name of the corresponding univalent radical, e.g. a naphthyl group with two points of attachment is termed naphthylidene. Aryl, however, does not encompass or overlap in any way with heteroaryl, separately defined below. Hence, if one or more carbocyclic aromatic rings is fused with a heterocycloalkyl aromatic ring, the resulting ring system is heteroaryl, not aryl, as defined herein.

As used herein, “aryloxy” refers to the group —O-aryl.

As used herein, “aralkyl” refers to the group -alkyl-aryl.

As used herein, “carbamimidoyl” refers to the group —C(═NH)—NH2.

As used herein, “substituted carbamimidoyl” refers to the group —C(═NRe)—NRfRg where

Re is chosen from hydrogen, cyano, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocycloalkyl; and

Rf and Rg are independently chosen from hydrogen optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocycloalkyl,

provided that at least one of Re, Rf, and Rg is not hydrogen and wherein substituted alkyl, cycloalkyl, aryl, heterocycloalkyl, and heteroaryl refer respectively to alkyl, cycloalkyl, aryl, heterocycloalkyl, and heteroaryl wherein one or more (such as up to 5, for example, up to 3) hydrogen atoms are replaced by a substituent independently chosen from

—Ra, —ORb, optionally substituted amino (including —NRcCORb, —NRcCO2Ra, —NRcCONRbRc, —NRbC(NRc)NRbRc, —NRbC(NCN)NRbRc, and —NRcSO2Ra), halo, cyano, nitro, oxo (as a substituent for cycloalkyl, heterocycloalkyl, and heteroaryl), optionally substituted acyl (such as —CORb), optionally substituted alkoxycarbonyl (such as —CO2Rb), aminocarbonyl (such as —CONRbRc), —OCORb, —OCO2Ra, OCONRbRc, OP(O)(ORb)ORc, sulfanyl (such as SRb), sulfinyl (such as —SORa), and sulfonyl (such as —SO2Ra and —SO2NRbRc), where Ra is chosen from optionally substituted C1-C6 alkyl, optionally substituted aryl, and optionally substituted heteroaryl;

Rb is chosen from H, optionally substituted C1-C6 alkyl, optionally substituted aryl, and optionally substituted heteroaryl; and

Rc is chosen from hydrogen and optionally substituted C1-C4 alkyl; or

Rb and Rc, and the nitrogen to which they are attached, form an optionally substituted heterocycloalkyl group; and

where each optionally substituted group is unsubstituted or independently substituted with one or more, such as one, two, or three, substituents independently chosen from C1-C4 alkyl, aryl, heteroaryl, aryl-C1-C4 alkyl-, heteroaryl-C1-C4 alkyl-, C1-C4 haloalkyl, —OC1-C4 alkyl, —OC1-C4 alkylphenyl, —C1-C4 alkyl-OH, —OC1-C4 haloalkyl, halo, —OH, —NH2, —C1-C4 alkyl-NH2, —N(C1-C4 alkyl)(C1-C4 alkyl), —NH(C1-C4 alkyl), —N(C1-C4 alkyl)(C1-C4 alkylphenyl), —NH(C1-C4 alkylphenyl), cyano, nitro, oxo (as a substituent for cycloalkyl, heterocycloalkyl, or heteroaryl), —CO2H, —C(O)OC1-C4 alkyl, —CON(C1-C4 alkyl)(C1-C4 alkyl), —CONH(C1-C4 alkyl), —CONH2, —NHC(O)(C1-C4 alkyl), —NHC(O)(phenyl), —N(C1-C4 alkyl)C(O)(C1-C4 alkyl), —N(C1-C4 alkyl)C(O)(phenyl), —C(O)C1-C4 alkyl, —C(O)C1-C4 phenyl, —C(O)C1-C4 haloalkyl, —OC(O)C1-C4 alkyl, —SO2(C1-C4 alkyl), —SO2(phenyl), —SO2(C1-C4 haloalkyl), —SO2NH2, —SO2NH(C1-C4 alkyl), —SO2 NH(phenyl), —NHSO2(C1-C4 alkyl), —NHSO2(phenyl), and —NHSO2(C1-C4 haloalkyl).

As used herein, “halo” refers to fluoro, chloro, bromo, and iodo, and the term “halogen” includes fluorine, chlorine, bromine, and iodine.

As used herein, “haloalkyl” refers to alkyl as defined above having the specified number of carbon atoms, substituted with 1 or more halogen atoms, up to the maximum allowable number of halogen atoms. Examples of haloalkyl include, but are not limited to, trifluoromethyl, difluoromethyl, 2-fluoroethyl, and penta-fluoroethyl.

As used herein, “heteroaryl” refers to:

5- to 7-membered aromatic, monocyclic rings containing one or more, for example, from 1 to 4, or in certain embodiments, from 1 to 3, heteroatoms chosen from N, O, and S, with the remaining ring atoms being carbon;

bicyclic heterocycloalkyl rings containing one or more, for example, from 1 to 4, or in certain embodiments, from 1 to 3, heteroatoms chosen from N, O, and S, with the remaining ring atoms being carbon and wherein at least one heteroatom is present in an aromatic ring; and

tricyclic heterocycloalkyl rings containing one or more, for example, from 1 to 5, or in certain embodiments, from 1 to 4, heteroatoms chosen from N, O, and S, with the remaining ring atoms being carbon and wherein at least one heteroatom is present in an aromatic ring.

For example, heteroaryl includes a 5- to 7-membered heterocycloalkyl, aromatic ring fused to a 5- to 7-membered cycloalkyl or heterocycloalkyl ring. For such fused, bicyclic heteroaryl ring systems wherein only one of the rings contains one or more heteroatoms, the point of attachment may be at either ring. When the total number of S and O atoms in the heteroaryl group exceeds 1, those heteroatoms are not adjacent to one another. In certain embodiments, the total number of S and O atoms in the heteroaryl group is not more than 2. In certain embodiments, the total number of S and O atoms in the aromatic heterocycle is not more than 1. Examples of heteroaryl groups include, but are not limited to, (as numbered from the linkage position assigned priority 1), 2-pyridyl, 3-pyridyl, 4-pyridyl, 2,3-pyrazinyl, 3,4-pyrazinyl, 2,4-pyrimidinyl, 3,5-pyrimidinyl, 2,3-pyrazolinyl, 2,4-imidazolinyl, isoxazolinyl, oxazolinyl, thiazolinyl, thiadiazolinyl, tetrazolyl, thienyl, benzothiophenyl, furanyl, benzofuranyl, benzoimidazolinyl, indolinyl, pyridazinyl, triazolyl, quinolinyl, pyrazolyl, and 5,6,7,8-tetrahydroisoquinolinyl. Bivalent radicals derived from univalent heteroaryl radicals whose names end in “-yl” by removal of one hydrogen atom from the atom with the free valence are named by adding “-idene” to the name of the corresponding univalent radical, e.g. a pyridyl group with two points of attachment is a pyridylidene. Heteroaryl does not encompass or overlap with aryl, cycloalkyl, or heterocycloalkyl, as defined herein

Substituted heteroaryl also includes ring systems substituted with one or more oxide (—O−) substituents, such as pyridinyl N-oxides.

As used herein, “heterocycloalkyl” refers to a single, non-aromatic ring, usually with 3 to 7 ring atoms, containing at least 2 carbon atoms in addition to 1-3 heteroatoms independently chosen from oxygen, sulfur, and nitrogen, as well as combinations comprising at least one of the foregoing heteroatoms. The ring may be saturated or have one or more carbon-carbon double bonds. Suitable heterocycloalkyl groups include, for example (as numbered from the linkage position assigned priority 1), 2-pyrrolidinyl, 2,4-imidazolidinyl, 2,3-pyrazolidinyl, 2-piperidyl, 3-piperidyl, 4-piperidyl, and 2,5-piperizinyl. Morpholinyl groups are also contemplated, including 2-morpholinyl and 3-morpholinyl (numbered wherein the oxygen is assigned priority 1). Substituted heterocycloalkyl also includes ring systems substituted with one or more oxo (═O) or oxide (—O−) substituents, such as piperidinyl N-oxide, morpholinyl-N-oxide, 1-oxo-1-thiomorpholinyl and 1,1-dioxo-1-thiomorpholinyl.

“Heterocycloalkyl” also includes bicyclic ring systems wherein one non-aromatic ring, usually with 3 to 7 ring atoms, contains at least 2 carbon atoms in addition to 1-3 heteroatoms independently chosen from oxygen, sulfur, and nitrogen, as well as combinations comprising at least one of the foregoing heteroatoms; and the other ring, usually with 3 to 7 ring atoms, optionally contains 1-3 heteratoms independently chosen from oxygen, sulfur, and nitrogen and is not aromatic.

As used herein, “modulation” refers to a change in activity as a direct or indirect response to the presence of a chemical entity as described herein, relative to the activity of in the absence of the chemical entity. The change may be an increase in activity or a decrease in activity, and may be due to the direct interaction of the compound with the a target or due to the interaction of the compound with one or more other factors that in turn affect the target's activity. For example, the presence of the chemical entity may, for example, increase or decrease the target activity by directly binding to the target, by causing (directly or indirectly) another factor to increase or decrease the target activity, or by (directly or indirectly) increasing or decreasing the amount of target present in the cell or organism.

As used herein, “sulfanyl” refers to the groups: —S-(optionally substituted (C1-C6)alkyl), —S-(optionally substituted aryl), —S-(optionally substituted heteroaryl), and —S-(optionally substituted heterocycloalkyl). Hence, sulfanyl includes the group C1-C6 alkylsulfanyl.

As used herein, “sulfinyl” refers to the groups: —S(O)-(optionally substituted (C1-C6)alkyl), —S(O)-optionally substituted aryl), —S(O)-optionally substituted heteroaryl), —S(O)-(optionally substituted heterocycloalkyl); and —S(O)-(optionally substituted amino).

As used herein, “sulfonyl” refers to the groups: —S(O2)-(optionally substituted (C1-C6)alkyl), —S(O2)-optionally substituted aryl), —S(O2)-optionally substituted heteroaryl), —S(O2)-(optionally substituted heterocycloalkyl), and —S(O2)-(optionally substituted amino).

As used herein, “substituted” refers to any one or more hydrogens on the designated atom or group is replaced with a selection from the indicated group, provided that the designated atom's normal valence is not exceeded. When a substituent is oxo (i.e. ═O) then 2 hydrogens on the atom are replaced. Combinations of substituents and/or variables are permissible only if such combinations result in stable compounds or useful synthetic intermediates. A stable compound or stable structure is meant to imply a compound that is sufficiently robust to survive isolation from a reaction mixture, and subsequent formulation as an agent having at least practical utility. Unless otherwise specified, substituents are named into the core structure. For example, it is to be understood that when (cycloalkyl)alkyl is listed as a possible substituent, the point of attachment of this substituent to the core structure is in the alkyl portion.

As used herein, the terms “substituted” alkyl, cycloalkyl, aryl, heterocycloalkyl, and heteroaryl, unless otherwise expressly defined, refer respectively to alkyl, cycloalkyl, aryl, heterocycloalkyl, and heteroaryl wherein one or more (such as up to 5, for example, up to 3) hydrogen atoms are replaced by a substituent independently chosen from

—Ra, —ORb, optionally substituted amino (including —NRcCORb, —NRcCO2Ra, —NRcCONRbRc, —NRbC(NRc)NRbRc, —NRbC(NCN)NRbRc, and —NRcSO2Ra), halo, cyano, azido, nitro, oxo (as a substituent for cycloalkyl or heterocycloalkyl), optionally substituted acyl (such as —CORb), optionally substituted alkoxycarbonyl (such as —CO2Rb), aminocarbonyl (such as —CONRbRc), —OCORb, —OCO2Ra, —OCONRbRc, —OP(O)(ORb)ORc, sulfanyl (such as SRb), sulfinyl (such as —SORa), and sulfonyl (such as —SO2Ra and —SO2NRbRc),

where Ra is chosen from optionally substituted C1-C6 alkyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted aryl, and optionally substituted heteroaryl;

Rb is chosen from hydrogen, optionally substituted C1-C6 alkyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, and optionally substituted heteroaryl; and

Rc is chosen from hydrogen and optionally substituted C1-C4 alkyl; or

Rb and Rc, and the nitrogen to which they are attached, form an optionally substituted heterocycloalkyl group; and

where each optionally substituted group is unsubstituted or independently substituted with one or more, such as one, two, or three, substituents independently chosen from C1-C4 alkyl, aryl, heteroaryl, aryl-C1-C4 alkyl-, heteroaryl-C1-C4 alkyl-, C1-C4 haloalkyl, —OC1-C4 alkyl, —OC1-C4 alkylphenyl, —C1-C4 alkyl-OH, —OC1-C4 haloalkyl, halo, —OH, —NH2, —C1-C4 alkyl-NH2, —N(C1-C4 alkyl)(C1-C4 alkyl), —NH(C1-C4 alkyl), —N(C1-C4 alkyl)(C1-C4 alkylphenyl), —NH(C1-C4 alkylphenyl), cyano, nitro, oxo (as a substituent for cycloalkyl or heterocycloalkyl), —CO2H, —C(O)OC1-C4 alkyl, —CON(C1-C4 alkyl)(C1-C4 alkyl), —CONH(C1-C4 alkyl), —CONH2, —NHC(O)(C1-C4 alkyl), —NHC(O)(phenyl), —N(C1-C4 alkyl)C(O)(C1-C4 alkyl), —N(C1-C4 alkyl)C(O)(phenyl), —C(O)C1-C4 alkyl, —C(O)C1-C4 alkylphenyl, —C(O)C1-C4 haloalkyl, —OC(O)C1-C4 alkyl, —SO2(C1-C4 alkyl), —SO2(phenyl), —SO2(C1-C4 haloalkyl), —SO2NH2, —SO2NH(C1-C4 alkyl), —SO2NH(phenyl), —NHSO2(C1-C4 alkyl), —NHSO2(phenyl), and —NHSO2(C1-C4 haloalkyl).

As used herein, “substituted acyl” refers to the groups (substituted alkyl)-C(O)—; (substituted cycloalkyl)-C(O)—; (substituted aryl)-C(O)—; (substituted heteroaryl)-C(O)—; and (substituted heterocycloalkyl)-C(O)—, wherein the group is attached to the parent structure through the carbonyl functionality and wherein substituted alkyl, cycloalkyl, aryl, heteroaryl, and heterocycloalkyl, refer respectively to alkyl, cycloalkyl, aryl, heteroaryl, and heterocycloalkyl wherein one or more (such as up to 5, for example, up to 3) hydrogen atoms are replaced by a substituent independently chosen from

—Ra, —ORb, optionally substituted amino (including —NRcCORb, —NRcCO2Ra, —NRcCONRbRc, —NRbC(NRc)NRbRc, —NRbC(NCN)NRbRc, and —NRcSO2Ra), halo, cyano, nitro, oxo (as a substituent for cycloalkyl or heterocycloalkyl), optionally substituted acyl (such as —CORb), optionally substituted alkoxycarbonyl (such as —CO2Rb), aminocarbonyl (such as —CONRbRc), —OCORb, —OCO2Ra, OCONRbRc, —OP(O)(ORb)ORc, sulfanyl (such as SRb), sulfinyl (such as —SORa), and sulfonyl (such as —SO2Ra and —SO2NRbRc),

where Ra is chosen from optionally substituted C1-C6 alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted aryl, and optionally substituted heteroaryl;

Rb is chosen from H, optionally substituted C1-C6 alkyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, and optionally substituted heteroaryl; and

Rc is chosen from hydrogen and optionally substituted C1-C4 alkyl; or

Rb and Rc, and the nitrogen to which they are attached, form an optionally substituted heterocycloalkyl group; and

where each optionally substituted group is unsubstituted or independently substituted with one or more, such as one, two, or three, substituents independently chosen from C1-C4 alkyl, aryl, heteroaryl, aryl-C1-C4 alkyl-, heteroaryl-C1-C4 alkyl-, C1-C4 haloalkyl, —OC1-C4 alkyl, —OC1-C4 alkylphenyl, —C1-C4 alkyl-OH, —OC1-C4 haloalkyl, halo, —OH, —NH2, —C1-C4 alkyl-NH2, —N(C1-C4 alkyl)(C1-C4 alkyl), —NH(C1-C4 alkyl), —N(C1-C4 alkyl)(C1-C4 alkylphenyl), —NH(C1-C4 alkylphenyl), cyano, nitro, oxo (as a substituent for cycloalkyl or heterocycloalkyl), —CO2H, —C(O)OC1-C4 alkyl, —CON(C1-C4 alkyl)(C1-C4 alkyl), —CONH(C1-C4 alkyl), —CONH2, —NHC(O)(C1-C4 alkyl), —NHC(O)(phenyl), —N(C1-C4 alkyl)C(O)(C1-C4 alkyl), —N(C1-C4 alkyl)C(O)(phenyl), —C(O)C1-C4 alkyl, —C(O)C1-C4 alkylphenyl, —C(O)C1-C4 haloalkyl, —OC(O)C1-C4 alkyl, —SO2(C1-C4 alkyl), —SO2(phenyl), —SO2(C1-C4 haloalkyl), —SO2NH2, —SO2NH(C1-C4 alkyl), —SO2NH(phenyl), —NHSO2(C1-C4 alkyl), —NHSO2(phenyl), and —NHSO2(C1-C4 haloalkyl).

As used herein, “substituted alkoxy” refers to alkoxy wherein the alkyl constituent is substituted (i.e. —O-(substituted alkyl)) wherein “substituted alkyl” refers to alkyl wherein one or more (such as up to 5, for example, up to 3) hydrogen atoms are replaced by a substituent independently chosen from

—Ra, —ORb, optionally substituted amino (including —NRcCORb, —NRcCO2Ra, —NRcCONRbRc, —NRbC(NRc)NRbRc, —NRbC(NCN)NRbRc, and —NRcSO2Ra), halo, cyano, nitro, oxo (as a substituent for cycloalkyl or heterocycloalkyl), optionally substituted acyl (such as —CORb), optionally substituted alkoxycarbonyl (such as —CO2Rb), aminocarbonyl (such as —CONRbRc), —OCORb, —OCO2Ra, OCONRbRc, OP(O)(ORb)ORc, sulfanyl (such as SRb), sulfinyl (such as —SORa), and sulfonyl (such as —SO2Ra and —SO2NRbRc),

where Ra is chosen from optionally substituted C1-C6 alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted aryl, and optionally substituted heteroaryl;

Rb is chosen from H, optionally substituted C1-C6 alkyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, and optionally substituted heteroaryl; and

Rc is chosen from hydrogen and optionally substituted C1-C4 alkyl; or

Rb and Rc, and the nitrogen to which they are attached, form an optionally substituted heterocycloalkyl group; and

where each optionally substituted group is unsubstituted or independently substituted with one or more, such as one, two, or three, substituents independently chosen from C1-C4 alkyl, aryl, heteroaryl, aryl-C1-C4 alkyl-, heteroaryl-C1-C4 alkyl-, C1-C4 haloalkyl, —OC1-C4 alkyl, —OC1-C4 alkylphenyl, —C1-C4 alkyl-OH, —OC1-C4 haloalkyl, halo, —OH, —NH2, —C1-C4 alkyl-NH2, —N(C1-C4 alkyl)(C1-C4 alkyl), —NH(C1-C4 alkyl), —N(C1-C4 alkyl)(C1-C4 alkylphenyl), —NH(C1-C4 alkylphenyl), cyano, nitro, oxo (as a substituent for cycloalkyl or heterocycloalkyl), —CO2H, —C(O)OC1-C4 alkyl, —CON(C1-C4 alkyl)(C1-C4 alkyl), —CONH(C1-C4 alkyl), —CONH2, —NHC(O)(C1-C4 alkyl), —NHC(O)(phenyl), —N(C1-C4 alkyl)C(O)(C1-C4 alkyl), —N(C1-C4 alkyl)C(O)(phenyl), —C(O)C1-C4 alkyl, —C(O)C1-C4 alkylphenyl, —C(O)C1-C4 haloalkyl, —OC(O)C1-C4 alkyl, —SO2(C1-C4 alkyl), —SO2(phenyl), —SO2(C1-C4 haloalkyl), —SO2NH2, —SO2NH(C1-C4 alkyl), —SO2NH(phenyl), —NHSO2(C1-C4 alkyl), —NHSO2(phenyl), and —NHSO2(C1-C4 haloalkyl).

In some embodiments, a substituted alkoxy group is “polyalkoxy” or —O-(optionally substituted alkylene)-(optionally substituted alkoxy), and includes groups such as —OCH2CH2OCH3, and residues of glycol ethers such as polyethyleneglycol, and —O(CH2CH2O)xCH3, where x is an integer of 2-20, such as 2-10, and for example, 2-5. Another substituted alkoxy group is hydroxyalkoxy or —OCH2(CH2)yOH, where y is an integer of 1-10, such as 1-4.

As used herein, “substituted alkoxycarbonyl” refers to the group (substituted alkyl)-O—C(O)— wherein the group is attached to the parent structure through the carbonyl functionality and wherein substituted refers to alkyl wherein one or more (such as up to 5, for example, up to 3) hydrogen atoms are replaced by a substituent independently chosen from

—Ra, —ORb, optionally substituted amino (including —NRcCORb, —NRcCO2Ra, —NRcCONRbRc, —NRbC(NRc)NRbRc, —NRbC(NCN)NRbRc, and —NRcSO2Ra), halo, cyano, nitro, oxo (as a substituent for cycloalkyl or heterocycloalkyl), optionally substituted acyl (such as —CORb), optionally substituted alkoxycarbonyl (such as —CO2Rb), aminocarbonyl (such as —CONRbRc), —OCORb, —OCO2Ra, —OCONRbRc, —OP(O)(ORb)ORc, sulfanyl (such as SRb), sulfinyl (such as —SORa), and sulfonyl (such as —SO2Ra and —SO2NRbRc),

where Ra is chosen from optionally substituted C1-C6 alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted aryl, and optionally substituted heteroaryl;

Rb is chosen from H, optionally substituted C1-C6 alkyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, and optionally substituted heteroaryl; and

Rc is chosen from hydrogen and optionally substituted C1-C4 alkyl; or

Rb and Rc, and the nitrogen to which they are attached, form an optionally substituted heterocycloalkyl group; and

where each optionally substituted group is unsubstituted or independently substituted with one or more, such as one, two, or three, substituents independently chosen from C1-C4 alkyl, aryl, heteroaryl, aryl-C1-C4 alkyl-, heteroaryl-C1-C4 alkyl-, C1-C4 haloalkyl, —OC1-C4 alkyl, —OC1-C4 alkylphenyl, —C1-C4 alkyl-OH, —OC1-C4 haloalkyl, halo, —OH, —NH2, —C1-C4 alkyl-NH2, —N(C1-C4 alkyl)(C1-C4 alkyl), —NH(C1-C4 alkyl), —N(C1-C4 alkyl)(C1-C4 alkylphenyl), —NH(C1-C4 alkylphenyl), cyano, nitro, oxo (as a substituent for cycloalkyl or heterocycloalkyl), —CO2H, —C(O)OC1-C4 alkyl, —CON(C1-C4 alkyl)(C1-C4 alkyl), —CONH(C1-C4 alkyl), —CONH2, —NHC(O)(C1-C4 alkyl), —NHC(O)(phenyl), —N(C1-C4 alkyl)C(O)(C1-C4 alkyl), —N(C1-C4 alkyl)C(O)(phenyl), —C(O)C1-C4 alkyl, —C(O)C1-C4 alkylphenyl, —C(O)C1-C4 haloalkyl, —OC(O)C1-C4 alkyl, —SO2(C1-C4 alkyl), —SO2(phenyl), —SO2(C1-C4 haloalkyl), —SO2NH2, —SO2NH(C1-C4 alkyl), —SO2NH(phenyl), —NHSO2(C1-C4 alkyl), —NHSO2(phenyl), and —NHSO2(C1-C4 haloalkyl).

As used herein, “substituted amino” refers to the group —NHRd or —NRdRe wherein Rd is chosen from hydroxy, optionally substituted alkoxy, optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted acyl, optionally substituted carbamimidoyl, aminocarbonyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocycloalkyl, optionally substituted alkoxycarbonyl, sulfinyl and sulfonyl, and wherein Re is chosen from optionally substituted alkyl, optionally substituted cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocycloalkyl; and wherein substituted alkyl, cycloalkyl, aryl, heterocycloalkyl, and heteroaryl refer respectively to alkyl, cycloalkyl, aryl, heterocycloalkyl, and heteroaryl wherein one or more (such as up to 5, for example, up to 3) hydrogen atoms are replaced by a substituent independently chosen from

—Ra, —ORb, optionally substituted amino (including —NRcCORb, —NRcCO2Ra, —NRcCONRbRc, —NRbC(NRc)NRbRc, —NRbC(NCN)NRbRc, and —NRcSO2Ra), halo, cyano, nitro, oxo (as a substituent for cycloalkyl or heterocycloalkyl), optionally substituted acyl (such as —CORb), optionally substituted alkoxycarbonyl (such as —CO2Rb), aminocarbonyl (such as —CONRbRc), —OCORb, OCO2Ra, —OCONbRc, OP(O)(ORb)ORc, sulfanyl (such as SRb), sulfinyl (such as —SORa), and sulfonyl (such as —SO2Ra and —SO2NRbRc),

where Ra is chosen from optionally substituted C1-C6 alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted aryl, and optionally substituted heteroaryl;

Rb is chosen from H, optionally substituted C1-C6 alkyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, and optionally substituted heteroaryl; and

Rc is chosen from hydrogen and optionally substituted C1-C4 alkyl; or

Rb and Rc, and the nitrogen to which they are attached, form an optionally substituted heterocycloalkyl group; and

where each optionally substituted group is unsubstituted or independently substituted with one or more, such as one, two, or three, substituents independently chosen from C1-C4 alkyl, aryl, heteroaryl, aryl-C1-C4 alkyl-, heteroaryl-C1-C4 alkyl-, C1-C4 haloalkyl, —OC1-C4 alkyl, —OC1-C4 alkylphenyl, —C1-C4 alkyl-OH, —OC1-C4 haloalkyl, halo, —OH, —NH2, —C1-C4 alkyl-NH2, —N(C1-C4 alkyl)(C1-C4 alkyl), —NH(C1-C4 alkyl), —N(C1-C4 alkyl)(C1-C4 alkylphenyl), —NH(C1-C4 alkylphenyl), cyano, nitro, oxo (as a substituent for cycloalkyl or heterocycloalkyl), —CO2H, —C(O)OC1-C4 alkyl, —CON(C1-C4 alkyl)(C1-C4 alkyl), —CONH(C1-C4 alkyl), —CONH2, —NHC(O)(C1-C4 alkyl), —NHC(O)(phenyl), —N(C1-C4 alkyl)C(O)(C1-C4 alkyl), —N(C1-C4 alkyl)C(O)(phenyl), —C(O)C1-C4 alkyl, —C(O)C1-C4 alkylphenyl, —C(O)C1-C4 haloalkyl, —OC(O)C1-C4 alkyl, —SO2(C1-C4 alkyl), —SO2(phenyl), —SO2(C1-C4 haloalkyl), —SO2NH2, —SO2NH(C1-C4 alkyl), —SO2NH(phenyl), —NHSO2(C1-C4 alkyl), —NHSO2(phenyl), and —NHSO2(C1-C4 haloalkyl); and

wherein optionally substituted acyl, optionally substituted alkoxycarbonyl, sulfinyl and sulfonyl are as defined herein.

The term “substituted amino” also refers to N-oxides of the groups —NHRd, and NRdRd each as described above. N-oxides can be prepared by treatment of the corresponding amino group with, for example, hydrogen peroxide or m-chloroperoxybenzoic acid. The person skilled in the art is familiar with reaction conditions for carrying out the N-oxidation.

Compounds of Formula I include, but are not limited to, optical isomers of compounds of Formula I, racemates, and other mixtures thereof. In those situations, the single enantiomers or diastereomers, i.e. optically active forms, can be obtained by asymmetric synthesis or by resolution of the racemates. Resolution of the racemates can be accomplished, for example, by conventional methods such as crystallization in the presence of a resolving agent, or chromatography, using, for example a chiral high-pressure liquid chromatography (HPLC) column. In addition, compounds of Formula I include Z- and E-forms (or cis- and trans-forms) of compounds with carbon-carbon double bonds. Where compounds of Formula I exists in various tautomeric forms, chemical entities described herein include all tautomeric forms of the compound.

Chemical entities described herein include, but are not limited to compounds of Formula I and all pharmaceutically acceptable forms thereof. Pharmaceutically acceptable forms of the chemical entities recited herein include pharmaceutically acceptable salts, solvates, crystal forms (including polymorphs and clathrates), chelates, non-covalent complexes, prodrugs, and mixtures thereof. In certain embodiments, the chemical entities described herein are in the form of pharmaceutically acceptable salts. Hence, the terms “chemical entity” and “chemical entities” also encompass pharmaceutically acceptable salts, solvates, chelates, non-covalent complexes, prodrugs, and mixtures.

“Pharmaceutically acceptable salts” include, but are not limited to salts with inorganic acids, such as hydrochloride, phosphate, diphosphate, hydrobromide, sulfate, sulfinate, nitrate, and like salts; as well as salts with an organic acid, such as malate, maleate, fumarate, tartrate, succinate, citrate, lactate, methanesulfonate, p-toluenesulfonate, 2-hydroxyethylsulfonate, benzoate, salicylate, stearate, and alkanoate such as acetate, HOOC—(CH2)n—COOH where n is 0-4, and like salts. Similarly, pharmaceutically acceptable cations include, but are not limited to sodium, potassium, calcium, aluminum, lithium, and ammonium.

In addition, if the compound of Formula I is obtained as an acid addition salt, the free base can be obtained by basifying a solution of the acid salt. Conversely, if the product is a free base, an addition salt, particularly a pharmaceutically acceptable addition salt, may be produced by dissolving the free base in a suitable organic solvent and treating the solution with an acid, in accordance with conventional procedures for preparing acid addition salts from base compounds. Those skilled in the art will recognize various synthetic methodologies that may be used to prepare non-toxic pharmaceutically acceptable addition salts.

As noted above, prodrugs also fall within the scope of chemical entities, for example ester or amide derivatives of the compounds of Formula I. The term “prodrugs” includes any chemical entities that become compounds of Formula I when administered to a patient, e.g. upon metabolic processing of the prodrug. Examples of prodrugs include, but are not limited to, acetate, formate, phosphate, and benzoate and like derivatives of functional groups (such as alcohol or amine groups) in the compounds of Formula I.

As used herein, “solvate” refers to the chemical entity formed by the interaction of a solvent and a compound. Suitable solvates are pharmaceutically acceptable solvates, such as hydrates, including monohydrates and hemi-hydrates.

As used herein, “chelate” refers to the chemical entity formed by the coordination of a compound to a metal ion at two (or more) points.

As used herein, “non-covalent complex” refers to the chemical entity formed by the interaction of a compound and another molecule wherein a covalent bond is not formed between the compound and the molecule. For example, complexation can occur through van der Waals interactions, hydrogen bonding, and electrostatic interactions (also called ionic bonding).

As used herein, “active agent” is used to indicate a chemical entity which has biological activity. In certain embodiments, an “active agent” is a compound having pharmaceutical utility. For example an active agent may be an anti-cancer therapeutic.

As used herein, “significant” refers to any detectable change that is statistically significant in a standard parametric test of statistical significance such as Student's T-test, where p<0.05.

As used herein, “therapeutically effective amount” of a chemical entity described herein refers to an amount effective, when administered to a human or non-human patient, to provide a therapeutic benefit such as amelioration of symptoms, slowing of disease progression, or prevention of disease.

As used herein, “treatment” or “treating” refers to any treatment of a disease in a patient, including:

    • a) preventing the disease, that is, causing the clinical symptoms of the disease not to develop;
    • b) inhibiting the disease;
    • c) slowing or arresting the development of clinical symptoms; and/or
    • d) relieving the disease, that is, causing the regression of clinical symptoms.

As used herein, “patient” refers to an animal, such as a mammal, that has been or will be the object of treatment, observation or experiment. The methods described herein can be useful in both human therapy and veterinary applications. In some embodiments, the patient is a mammal; in some embodiments the patient is human; and in some embodiments the patient is chosen from cats and dogs.

Provided is at least one chemical entity chosen from compounds of Formula I

and pharmaceutically acceptable salts thereof wherein

R1 is selected from hydrogen, optionally substituted alkyl, cyano, halo, azido, optionally substituted amino, optionally substituted alkoxy, optionally substituted aryloxy, optionally substituted alkoxycarbonyl, optionally substituted aminocarbonyl, optionally substituted aminosulfonyl, sulfonyl, sulfinyl, and sulfanyl;

Z1 is selected from optionally substituted aryl, optionally substituted heteroaryl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, cyano, optionally substituted alkyl, optionally substituted acyl, optionally substituted alkoxycarbonyl, optionally substituted amino, optionally substituted aminocarbonyl, optionally substituted aminosulfonyl, optionally substituted carbamimidoyl, optionally substituted alkoxy, optionally substituted aryloxy, optionally substituted heteroaryloxy, optionally substituted heterocycloalkyloxy, optionally substituted alkenyl, optionally substituted alkynyl, sulfonyl, sulfinyl, and sulfanyl;

Z2 is selected from optionally substituted amidino, carboxyl, optionally substituted alkoxy carbonyl, optionally substituted acyl, optionally substituted alkenyl, optionally substituted alkyl, optionally substituted heterocycloalkyl, optionally substituted heteroaryl, and optionally substituted aminocarbonyl;

Z3 is chosen from hydrogen and optionally substituted alkyl; and

R3 is chosen from hydrogen and optionally substituted alkyl.

In some embodiments, Z1 is chosen from heteroaryl and phenyl, each of which is optionally substituted with one, two or three groups chosen from halo, optionally substituted lower alkyl, and optionally substituted lower alkoxy. In some embodiments, Z1 is chosen from pyrazolyl, phenyl, and phenyl substituted with one, two, or three groups chosen from halo, optionally substituted lower alkyl, and optionally substituted lower alkoxy. In some embodiments, Z1 is chosen from pyrazolyl, phenyl, and phenyl substituted with one, two, or three halo groups. In some embodiments, Z1 is chosen from pyrazolyl, phenyl, 3-fluorophenyl, 4-fluorophenyl, and 3,4-difluorophenyl.

In some embodiments, Z2 is aminocarbonyl. In some embodiments, Z2 is —C(O)—NHR4 wherein R4 is optionally substituted lower alkyl. In some embodiments, R4 is chosen from lower alkyl optionally substituted with phenyl, pyridyl, and lower alkoxy. In some embodiments, R4 is chosen from 2-methoxyethyl, benzyl, isopropyl, pyridin-2-ylmethyl, pyridin-3-ylmethyl, and pyridin-4-ylmethyl.

In some embodiments, Z3 is chosen from ethyl, methyl and propyl, each of which is substituted with a group independently selected from optionally substituted aryl, optionally substituted heteroaryl, optionally substituted cycloalkyl and optionally substituted heterocycloalkyl. In some embodiments, Z3 is chosen from 2-(phenyl)ethyl, benzyl, 2-(pyridin-2-yl)ethyl, and pyridin-2-ylmethyl, each of which is optionally substituted. In some embodiments, Z3 is chosen from 2-(phenyl)ethyl, benzyl, 2-(pyridin-2-yl)ethyl, and pyridin-2-ylmethyl, each of which is optionally substituted with one or two groups chosen from lower alkyl, lower alkoxy, halo, and hydroxy. In some embodiments, Z3 is chosen from 2-(3-fluorophenyl)ethyl, 2-(3-methylphenyl)ethyl, 2-(pyridin-2-yl)ethyl, 2-(3-methylphenyl)ethyl and pyridin-2-ylmethyl.

In some embodiments, R1 is chosen from hydrogen and optionally substituted lower alkyl. In some embodiments, R1 is chosen from hydrogen and lower alkyl. In some embodiments, R1 is chosen from hydrogen and methyl. In some embodiments, R1 is hydrogen.

In some embodiments, R3 is chosen from hydrogen and optionally substituted lower alkyl. In some embodiments, R3 is chosen from hydrogen and lower alkyl. In some embodiments, R3 is chosen from hydrogen and methyl. In some embodiments, R3 is hydrogen.

In some embodiments, the compound of Formula I is chosen from

{2-(3,4-difluorophenyl)-4-[(2-(2- pyridyl)ethyl)amino]pyrimidin-5-yl}-N-(2- methoxyethyl)carboxamide (2-(3,4-difluorophenyl)-4-{[2-(3- methylphenyl)ethyl]amino}pyrimidin-5-yl)-N-(3- pyridylmethyl)carboxamide {2-(3,4-difluorophenyl)-4-[(2-(2- pyridyl)ethyl)amino]pyrimidin-5-yl}-N-(3- pyridylmethyl)carboxamide {2-(3,4-difluorophenyl)-4-[(2-(2- pyridyl)ethyl)amino]pyrimidin-5-yl}-N- (methylethyl)carboxamide {2-(3,4-difluorophenyl)-4-[(2-(2- pyridyl)ethyl)amino]pyrimidin-5-yl}-N-benzylcarboxamide {2-(3,4-difluorophenyl)-4-[(2-(2- pyridyl)ethyl)amino]pyrimidin-5-yl}-N-(4- pyridylmethyl)carboxamide (2-(3,4-difluorophenyl)-4-{[2-(3- methylphenyl)ethyl]amino}pyrimidin-5-yl)-N-(2- methoxyethyl)carboxamide (2-(3,4-difluorophenyl)-4-{[2-(3- methylphenyl)ethyl]amino}pyrimidin-5-yl)-N-(4- pyridylmethyl)carboxamide (2-(3,4-difluorophenyl)-4-{[2-(3- methylphenyl)ethyl]amino}pyrimidin-5-yl)-N-(2- pyridylmethyl)carboxamide {2-(3,4-difluorophenyl)-4-[(2-(2- pyridyl)ethyl)amino]pyrimidin-5-yl}-N-(2- pyridylmethyl)carboxamide (4-{[2-(3-fluorophenyl)ethyl]amino}-2-pyrazol-4- ylpyrimidin-5-yl)-N-(2-pyridylmethyl)carboxamide (4-{[2-(3-fluorophenyl)ethyl]amino}-2-pyrazol-4- ylpyrimidin-5-yl)-N-(3-pyridylmethyl)carboxamide

Many of the optionally substituted starting compounds and other reactants are commercially available, e.g. from Aldrich Chemical Company (Milwaukee, Wis.) or can be readily prepared by those skilled in the art using commonly employed synthetic methodology.

The chemical entities described herein can be synthesized utilizing techniques well known in the art from commercially available starting materials and reagents. For example, the chemical entities described herein can be prepared as illustrated below with reference to the examples and reaction schemes.

Referring to Scheme 1, Step 1, a compound of Formula 101 is converted to the corresponding N-hydroxyimidamide through reaction with, for example, hydroxylamine hydrochloride. The N-hydroxyimidamide is isolated and hydrogenated to the corresponding imidamide using, for example, Pd/C as catalyst. The product, a compound of Formula 102, is isolated and optionally purified.

Referring to Scheme 1, Step 2, a compound of Formula 102 is converted to the corresponding 4-hydroxy pyrimidine though reaction with, for example, a compound of Formula 103 in ethanol. The product, a compound of Formula 104, is isolated and optionally purified.

Referring to Scheme 1, Step 3, a compound of Formula 104 is converted to the corresponding 4-chloropyrimidine through reaction, for example, with phosphorous oxychloride. The product, a compound of Formula 105, is isolated and optionally purified.

Referring to Scheme 1, Step 4, a compound of Formula 105 is converted to the corresponding 4-aminopyrimidine using, for example, an appropriately substituted amine. The product, a compound of Formula 106, is isolated and optionally purified.

Referring to Scheme 1, Step 5, a compound of Formula 106 is first saponified to a carboxylic acid using, for example, NaOH in THF/EtOH. The resulting acid is isolated, converted to the corresponding acid chloride using, for example, oxalyl chloride, and finally to the resulting amide through addition of an appropriately substituted amine. The product, a compound of Formula 107, is isolated and optionally purified.

Referring to Scheme 2, Step 1, a compound of Formula 201 is converted to the corresponding 2,4-dichloropyrimidine using standard chlorination conditions, for example, refluxing phosphorous oxychloride. The resulting 2,4-dichloropyrimidine is isolated and converted to the corresponding 4-aminopyrimidine through reaction with an appropriately substituted amine. The product, a compound of Formula 202, is isolated and optionally purified.

Referring to Scheme 2, Step 2, a compound of Formula 202 is first saponified to the corresponding carboxylic acid using, for example, NaOH. The resulting 2-chloro-pyrimidine-5-carboxylic acid is then isolated and subjected to a coupling reaction using, for example, a boronic acid. The product, a compound of Formula 203, is isolated and optionally purified.

Referring to Scheme 2, Step 3, a compound of Formula 203 is coupled to an amine using standard amide coupling conditions, such as HOBt/HBTU. The product, a compound of Formula 204, is isolated and purified.

Unless specified to the contrary, the reactions described herein take place at atmospheric pressure, generally within a temperature range from −10° C. to 200° C. Further, except as employed in the examples or as otherwise specified, reaction times and conditions are intended to be approximate, e.g. taking place at about atmospheric pressure within a temperature range of about −10° C. to about 110° C. over a period of about 1 to about 24 hours; reactions left to run overnight average a period of about 16 hours. For each gram of the limiting reagent, one cc (or mL) of solvent constitutes a volume equivalent.

The terms “solvent,” “organic solvent,” and “inert solvent” each mean a solvent inert under the conditions of the reaction being described in conjunction therewith [including, for example, benzene, toluene, acetonitrile, tetrahydrofuran (“THF”), dimethylformamide (“DMF”), chloroform, methylene chloride (or dichloromethane), diethyl ether, methanol, N-methylpyrrolidone (“NMP”), pyridine and the like]. Unless specified to the contrary, the solvents used in the reactions described herein are inert organic solvents. Unless specified to the contrary, for each gram of the limiting reagent, one cc (or mL) of solvent constitutes a volume equivalent.

Isolation and purification of the compounds and intermediates described herein can be effected, if desired, by any suitable separation or purification procedure such as, for example, filtration, extraction, crystallization, column chromatography, thin-layer chromatography or thick-layer chromatography, or a combination of these procedures. Specific illustrations of suitable separation and isolation procedures can be had by reference to the examples hereinbelow. However, other equivalent separation or isolation procedures can also be used.

When desired, the (R) and (S) isomers may be resolved by methods known to those skilled in the art, for example by formation of diastereoisomeric salts or complexes which may be separated, for example, by crystallization; via formation of diastereoisomeric derivatives which may be separated, for example, by crystallization, gas-liquid or liquid chromatography; selective reaction of one enantiomer with an enantiomer-specific reagent, for example enzymatic oxidation or reduction, followed by separation of the modified and unmodified enantiomers; or gas-liquid or liquid chromatography in a chiral environment, for example on a chiral support, such as silica with a bound chiral ligand or in the presence of a chiral solvent. It will be appreciated that when the desired enantiomer is converted into another chemical entity by one of the separation procedures described above, a further step may be required to liberate the desired enantiomeric form. Alternatively, a specific enantiomer may be synthesized by asymmetric synthesis using optically active reagents, substrates, catalysts and/or solvents, or by converting one enantiomer to the other by asymmetric transformation.

The chemical entities described herein may be useful in a variety of applications involving smooth muscle cells and/or non-muscle cells. In certain embodiments, the chemical entities may be used to inhibit smooth muscle myosin. The chemical entities may be useful to bind to, and/or inhibit the activity of, smooth muscle myosin. In certain embodiments, the smooth muscle myosin is human, although the chemical entities may be used to bind to or inhibit the activity of smooth muscle myosin from other organisms, such as other mammals.

In certain embodiments, the chemical entities may be used to inhibit non-muscle myosin. The chemical entities may be useful to bind to, and/or inhibit the activity of, non-muscle myosin. In certain embodiments, the non-muscle myosin is human, although the chemical entities may be used to bind to or inhibit the activity of non-muscle myosin from other organisms, such as other mammals.

The chemical entities described herein may be used to treat disease states associated with smooth muscle and/or non-muscle myosin. Such disease states which can be treated by the chemical entities described herein include, but are not limited to, hypertension, asthma, incontinence, chronic obstructive pulmonary disorder, pre-term labor, and the like. It is appreciated that in some cases the cells may not be in an abnormal state and still require treatment. Thus, in certain embodiments, the chemical entities described herein are applied to cells or administered to individuals afflicted or subject to impending affliction with any one of these disorders or states.

More specifically, the chemical entities described herein may be useful for the treatment of diseases or symptoms related to abnormal increased muscle tone or excessive contraction, or spasm of vascular smooth muscle in systemic, coronary, pulmonary circulation, and micro-circulatory smooth muscle as well, such as systemic hypertension, malignant hypertension, hypertension crisis, symptomatic hypertension, pulmonary hypertension, pulmonary infarction, angina pectoris, cardiac infarction, micro-circulation malfunction under shock condition, and infarction occurred in other location or organs of the human or animal body. Other diseases or symptoms that can be treated with the chemical entities described herein include:

spasm of gastro-intestine smooth muscle, including sphincters, such as gastric spasm, pylorospasm, and spasms of biliary tract, pancreatic tract, urinary tract, caused by inflammation, stimulation of stones or parasites;
spasm of other visceral organs such as uterus, Fallopian tube, and so on;
spasm of trachea-bronchial tree smooth muscle, diaphragm muscle, such as various asthma, breathlessness, dyspnea, diaphragmatic convulsion, and so on;
spasm of alimentary canal smooth muscle, including stomach, intestine and colons, biliary and pancreatic duct etc.; and
spasm of urinary tract smooth muscle.

In addition, the chemical entities described herein can be used for control, management and manipulation of labor during pregnancy. The method is particularly useful for inhibition of spontaneous preterm labor which would, if untreated, result in premature delivery or abortion and for inhibition of surgically induced labor during transuterine fetal surgery. The method is also useful for inducing the labor in overterm pregnancies where the labor does not occur on term and when it is necessary to induce labor in order to assure the normal delivery.

Further, the chemical entities described herein can be used for the treatment of “airway wall remodeling”, which is a condition associated with diseases or conditions characterized by airway wall thickening and air obstruction, which may, for example occur in the small airways of patients with certain respiratory disease conditions, such as, chronic obstructive pulmonary disease (COPD).

Other disease states which can be treated by the chemical entities, compositions and methods provided herein also include, but are not limited to glaucoma and other ocular indications. More specifically, chemical entities described herein may be useful for the treatment of diseases or symptoms related to glaucoma, including increased intraocular pressure, reduced flow of intraocular aqueous humor, and optical nerve damage. Other diseases or symptoms that can be treated with the chemical entities, compositions, and methods described herein including intraocular hypertension.

ATP hydrolysis is employed by myosin to produce force. An increase in ATP hydrolysis would correspond to an increase in the force or velocity of muscle contraction. In the presence of actin, myosin ATPase activity is stimulated more than 100-fold. Thus, the measurement of ATP hydrolysis not only measures myosin enzymatic activity but also its interaction with the actin filament. Assays for such activity may employ smooth muscle myosin from a human source, although myosin from other organisms can also be used. Systems that model the regulatory role of calcium in myosin binding may also be used.

The in vitro rate of ATP hydrolysis correlates to smooth muscle myosin potentiating activity, which can be determined by monitoring the production of either ADP or phosphate, for example as described in U.S. Pat. No. 6,410,254. ADP production can also be monitored by coupling the ADP production to NADH oxidation (using, for example, the enzymes pyruvate kinase and lactate dehydrogenase) and monitoring the NADH level, by example, either by absorbance or fluorescence (Greengard, P., Nature 178 (Part 4534): 632-634 (1956); Mol Pharmacol 1970 January; 6(1):31-40). Phosphate production can be monitored using purine nucleoside phosphorylase to couple phosphate production to the cleavage of a purine analog, which results in either a change in absorbance (Proc Natl Acad Sci USA 1992 Jun. 1; 89(11):4884-7) or fluorescence (Biochem J 1990 Mar. 1; 266(2):611-4). While a single measurement is employed, multiple measurements of the same sample at different times in order may be used to determine the absolute rate of the protein activity; such measurements have higher specificity particularly in the presence of test compounds that have similar absorbance or fluorescence properties with those of the enzymatic readout.

Test compounds may be assayed in a highly parallel fashion using multiwell plates by placing the compounds either individually in wells or testing them in mixtures. Assay components including the target protein complex, coupling enzymes and substrates, and ATP may then be added to the wells and the absorbance or fluorescence of each well of the plate can be measured with a plate reader.

One method uses a 384 well plate format and a 25 μL reaction volume. A pyruvate kinase/lactate dehydrogenase coupled enzyme system (Huang T G and Hackney D D. (1994) J Biol Chem 269(23):16493-16501) is used to measure the rate of ATP hydrolysis in each well. As will be appreciated by those of skill in the art, the assay components are added in buffers and reagents. Since the methods outlined herein allow kinetic measurements, incubation periods may be optimized to give adequate detection signals over the background. The assay is performed in real time to give the kinetics of ATP hydrolysis to increase the signal-to-noise ratio of the assay.

Selectivity for smooth muscle myosin may be determined by substituting other myosins in one or more of the above-described assays and comparing the results obtained against those obtained using the cardiac equivalents.

Chemical entities identified by the methods described herein as smooth muscle myosin modulators may be further tested in an efficacy screen, such as a screen using strips of permeabilized smooth muscle from, e.g., chicken gizzard. Calcium-sensitive smooth muscle strips are prepared by dissecting chicken gizzard tissue, followed by treatment with 1% Triton X-100 to make the strips permeable to exogenous compounds (Barsotti, R J, et al., Am J. Physiol. 1987 May; 252(5 Pt 1):C543-54). These strips can be stored in 50% glycerol for several weeks at −20° C., allowing multiple experiments to be performed with each batch of muscle strips. Experiments are performed using a solution of 20 mM imidazole pH 7.0, 5.5 mM ATP, 7 mM MgCl2, 55 mM KCl, 1 μM Calmodulin, and 10 mM EGTA. Free calcium will be controlled by addition of various amounts of CaCl2, according to the calculations of MAXChelator (Patton, et al. Cell Calcium. 35/5 pp. 427-431, 2004). An isometric muscle fiber apparatus is used to measure isometric tension, for example using an Aurora Scientific 400A transducer with National Instruments PCI-MIO-16E-4, 16 channels, 12 bit A/D board for data acquisition. The chemically skinned gizzard fibers are relaxed when bathed in low calcium solutions (pCa 8), but develop isometric tension when the free calcium of the bathing solution is increased to pCa 5. These fibers can be repeatedly contracted and relaxed by switching between high and low calcium bathing solutions.

Compounds are first tested for their ability to prevent contraction of gizzard strips, by preincubating relaxed fibers with a compound, followed by transfer to high calcium solution containing the compound. Next, compounds are tested for their ability to cause relaxation of contracting fibers by adding the compound to fibers already incubating in high calcium solution. Washout experiments are performed to ensure that the inhibitory effects are reversible, so that the compounds do not cause denaturation or other irreparable damage to the smooth muscle myosin.

The chemical entities are administered at a therapeutically effective dosage, e.g., a dosage sufficient to provide treatment of the disease states previously described. Generally, a daily dose is from about 0.05 to about 100 mg/kg of body weight, such as from about 0.10 to about 10 mg/kg of body weight or from about 0.15 to about 1 mg/kg of body weight. Thus, for administration to a 70 kg person, the dosage range is from about 3.5 to about 7000 mg per day, such as from about 7 to about 700 mg per day or from about 10 to about 100 mg per day. The amount of active chemical entity administered will, of course, be dependent on the subject and disease state being treated, the severity of the affliction, the manner and schedule of administration and the judgment of the prescribing physician; for example, a dose range for oral administration may be from about 70 to about 700 mg per day, whereas for intravenous administration the dose range may be from about 700 to about 7000 mg per day. The active agents may be chosen for longer or shorter plasma half-lives, respectively.

Administration of the chemical entities described herein can be via any of the accepted modes of administration for agents that serve similar utilities including, but not limited to, orally, subcutaneously, intravenously, intranasally, topically, transdermally, sublingually, intramucosally, intraperitoneally, intramuscularly, intrapulmonarilly, vaginally, rectally, and intraocularly (including intraocular injection). Oral, topical, parenteral, and intraocular administration are customary in treating many of the indications recited herein.

Pharmaceutical compositions include solid, semi-solid, liquid and aerosol dosage forms, such as, e.g., tablets, capsules, powders, liquids, suspensions, suppositories, aerosols, and the like. The chemical entities can also be administered in sustained- or controlled-release dosage forms, including depot injections, osmotic pumps, pills, transdermal (including electrotransport) patches, drops and the like, for prolonged and/or timed, pulsed administration at a predetermined rate. The compositions may be provided in unit dosage forms suitable for single administration of a precise dose.

The chemical entities may be administered either alone or in combination with a conventional pharmaceutical carrier or the like (e.g., mannitol, lactose, starch, magnesium stearate, sodium saccharine, talcum, cellulose, sodium crosscarmellose, glucose, gelatin, sucrose, magnesium carbonate, and the like). If desired, the pharmaceutical composition may also contain minor amounts of nontoxic auxiliary substances such as wetting agents, emulsifying agents, solubilizing agents, pH buffering agents and the like (e.g., sodium acetate, sodium citrate, cyclodextrine derivatives, sorbitan monolaurate, triethanolamine acetate, triethanolamine oleate. Generally, depending on the intended mode of administration, the pharmaceutical composition may contain from about 0.005% to about 95%, for example, from about 0.5% to about 50%, by weight of at least one chemical entity described herein. Actual methods of preparing such dosage forms are known or will be apparent, to those skilled in this art; for example, see Remington's Pharmaceutical Sciences, Mack Publishing Company, Easton, Pa.

In addition, the chemical entities may be co-administered with, and the pharmaceutical compositions can include, other medicinal agents, pharmaceutical agents, adjuvants, and the like.

In certain embodiments, the compositions are in the form of a pill or tablet and contain, along with the active ingredient, one or more of a diluent such as lactose, sucrose, dicalcium phosphate, and the like; a lubricant such as magnesium stearate or the like; and a binder such as starch, gum acacia, polyvinylpyrrolidine, gelatin, cellulose, cellulose derivatives and the like. In another solid dosage form, a powder, marume, solution or suspension (e.g., in propylene carbonate, vegetable oils or triglycerides) may be encapsulated in a gelatin capsule.

Liquid pharmaceutical compositions may, for example, be prepared by dissolving, dispersing, etc. at least one chemical entity and one or more optional pharmaceutical adjuvants in a carrier (e.g., water, saline, aqueous dextrose, glycerol, glycols, ethanol and the like) to form a solution or suspension. Injectables may be prepared in conventional forms, either as liquid solutions or suspensions, as emulsions, or in solid forms suitable for dissolution or suspension in liquid prior to injection. The percentage of chemical entities contained in such parenteral compositions is highly dependent on the specific nature thereof, as well as the activity of the chemical entities and the needs of the subject. However, percentages of active ingredient ranging from about 0.01% to about 10% in solution may be used, and may be higher if the composition is a solid which will be subsequently diluted to the above percentages. In certain embodiments, the composition has from about 0.2% to about 2% of the active agent in solution.

Compositions comprising at least one chemical entity may be administered intraocularly (including intraocular, periocular, and retrobulbar injection and perfusion). When administered intraocularly the sterile composition is typically aqueous. An appropriate buffer system may be added to prevent pH drift under storage conditions. When administered during intraocular surgical procedures, such as retrobulbar or periocular injection and intraocular perfusion or injection, the use of balanced salt irrigating solutions may be necessary. When used in a multidose form, preservatives may be required to prevent microbial contamination during use.

Compositions comprising at least one chemical entity may also be administered topically as eye drops, eye wash, creams, ointments, gels, and sprays. When administered as eye drops or eye wash, the active ingredients are typically dissolved or suspended in suitable carrier, typically a sterile aqueous solvent. An appropriate buffer system may be added to prevent pH drift under storage conditions. When used in a multidose form, preservatives may be required to prevent microbial contamination during use.

Compositions comprising at least one chemical entity may also be administered to the respiratory tract as an aerosol or in a solution for a nebulizer, or as a microfine powder for insufflation, alone or in combination with an inert carrier such as lactose. The particles of the composition typically have diameters of less than 50 microns, for example, less than 10 microns.

EXAMPLES

The following examples serve to more fully describe the manner of using the invention. These examples are presented for illustrative purposes and should not serve to limit the true scope of the invention.

Example I Preparation of 2-(3,4-difluorophenyl)-4-(2-(pyridin-2-yl)ethylamino)-N-(pyridin-3-ylmethyl)pyrimidine-5-carboxamide

2-(3,4-difluorophenyl)-4-(2-(pyridin-2-yl)ethylamino)-N-(pyridin-3-ylmethyl)pyrimidine-5-carboxamide

A three-necked RB flask was charged with 3,4-difluorobenzonitrile (20 g, 144 mmol) and a mixture of EtOH (190 mL) and water (10 mL). To this homogenous solution were added hydroxylamine hydrochloride (22 g, 317 mg) and TEA (48 mL, 331 mmol). The reaction mixture was stirred at r.t. for 30 min followed by heating to 85° C. for 1 h. TLC indicated the reaction was complete. The mixture was transferred to a 500 mL RB flask, concentrated under reduced pressure to almost dryness, added water (50 mL) and stirred for 30 min. The white precipitates were collected and air dry 12 h before use. LRMS (M+H+) m/z 173.0.

3,4-difluoro-N-hydroxybenzimidamide (21.1 g, 122.6 mmol) was taken into a solution of acetic acid (100 mL) and acetic anhydride (20 mL) along with Pd/C (500 mg, 10% wt.). The mixture was hydrogenated at 50 psi for 54 h. LC/MS indicated the reaction was complete. The mixture was filtered and the filtrate was concentrated under reduced pressure. The residue was then stirred in a mixture of EtOAc and hexanes (200 mL, 1/1) for 20 min. The solid was collected and dried under vacuum overnight to obtain 3,4-difluorobenzimidamide acetate as acetic acid salt (25.5 g, 96%). LRMS (M+H+) m/z 157.0.

To a 500 mL RB flask charged with EtOH (200 mL) was added sodium (2.0 g, 86.9 mmol, 3.7 equiv.) slowly. Once all the Na was dissolved in EtOH, 3,4-difluoro-N-hydroxybenzimidamide (5 g, 23.1 mmol, 1.0 equiv.) was added in three portions and the mixture was stirred at r.t. for 30 min followed by addition of diethyl 2-(ethoxymethylene)malonate (5.5 g, 25.4 mmol, 1.1 equiv.) in a period of 1 h. The reaction mixture was stirred for 1 h. LC/MS indicated the reaction was complete. The reaction mixture was quenched with AcOH (6 mL), concentrated under reduced pressure to about 50 mL, added a mixture of EtOAc and hexanes (200 mL, 3/7), and stirred for 30 min. The solid was collected to give ethyl 2-(3,4-difluorophenyl)-4-hydroxypyrimidine-5-carboxylate (8.2 g 96%).

To a mixture of ethyl 2-(3,4-difluorophenyl)-4-hydroxypyrimidine-5-carboxylate (3.3 g, 11.8 mmol) and N,N-diethylbenzenamine (3.0 mL) was added POCl3 (1.0 mL) and the reaction was reflux overnight. The mixture was then cooled to 0° C. and slowly added into an ice-water mixture with vigorous stirring. The aqueous solution was extracted with ether three times. The combined organic layer was washed with NaHCO3 and brine, dried over Na2SO4, and filtered. The filtrate was concentrated under reduced pressure and used without further purification.

To a solution of ethyl 4-chloro-2-(3,4-difluorophenyl)pyrimidine-5-carboxylate (1.2 g, 4.01 mmol) in DMF (8.0 mL) were added 2-aminoethylpyridine (540 mg, 4.42 mmol) and TEA (1.1 mL, 8.02 mmol). The mixture was stirred at r.t. for 30 min. LC/MS indicated the reaction was complete. The reaction was diluted with EtOAc (60 mL) and water (10 mL). The organic layer was separated, washed with sat. NH4Cl, water, and brine, dried over Na2SO4, and filtered. The filtrate was concentrated under reduced pressure. The crude was purified on Biotage 25 M using a mixture of EtOAc and hexanes to give ethyl 2-(3,4-difluorophenyl)-4-(2-(pyridin-2-yl)ethylamino)pyrimidine-5-carboxylate (1.35, 97%). LRMS (M+H+) m/z 385.1.

To a solution of ethyl 2-(3,4-difluorophenyl)-4-(2-(pyridin-2-yl)ethylamino)pyrimidine-5-carboxylate (1.2 g, 3.1 mmol) in a mixture of THF and EtOH (20 mL, 1/1) was added NaOH (10 mL, 10 mmol). The mixture was heated to 60° C. for 2 h. TLC indicated the reaction was complete. The mixture was concentrated to one third of its volume and acidified to pH 5. The solid was collected and dried under vacuum to give 2-(3,4-difluorophenyl)-4-(2-(pyridin-2-yl)ethylamino)pyrimidine-5-carboxylic acid (1.1 g, 98%). LRMS (M+H+) m/z 357.0.

To a solution of 2-(3,4-difluorophenyl)-4-(2-(pyridin-2-yl)ethylamino)pyrimidine-5-carboxylic acid (40 mg, 0.11 mmol, 1 equiv.) in DCM (10 mL) and 1 drop of DMF was added oxalyl chloride (65 uL, 0.13 mmol, 1.2 equiv.). The mixture was stirred at r.t. for 1 h followed by addition of 3-aminomethylpyridine (15 mg, 0.14 mmol, 1.4 equiv.) and TEA (31 uL, 0.22 mmol, 2.0 equiv.). The reaction mixture was stirred at r.t. for 1 h. LC/MS indicated the reaction was complete. The crude was concentrated under reduced pressure, redissolved in DMF/MeOH mixture, and filtered. The filtrate was purified on RP-HPLC using a mixture of acetonitrile and H2O to give 2-(3,4-difluorophenyl)-4-(2-(pyridin-2-yl)ethylamino)-N-(pyridin-3-ylmethyl)pyrimidine-5-carboxamide as a desired product (14.3 mg, 29%). LRMS (M+H+) m/z 447.1.

Example II Preparation of 2-(3-fluorophenethylamino)-6-(1H-pyrazol-4-yl)-N-(pyridin-2-ylmethyl)nicotinamide

4-(3-fluorophenethylamino)-2-(1H-pyrazol-4-yl)-N-(pyridin-2-ylmethyl)pyrimidine-5-carboxamide

A mixture of 5-carbeoxyuracil (3.01 g, 16.34 mmol), POCl3 (27 mL) and N,N-diethylaniline (4.5 mL) was stirred and refluxed for 2 h until 5-carbeoxyuracil was completely consumed. The mixture was cooled to r.t. and poured into ice-water (50 mL) and extracted with ether (2×100 mL). The ether solution was washed with saturated sodium bicarbonate, followed by brine. After concentration, the desired product was obtained as a brownish liquid in quantitative yield (3.6 g). LRMS (M+H+) m/z 221.0.

To a mixture of ethyl 2,4-dichloropyrimidine-5-carboxylate (1.33 g, 6.0 mmol) and DMF (12 mL) was added 3-fluorophenethyl amine (0.783 mL, 6.0 mmol), followed by DIEA (2.1 mL, 12 mmol). The mixture was stirred at r.t. for 2 hours. Concentration of the mixture followed by the purification on RP-HPLC using a mixture of acetonitrile and H2O gave ethyl 2-chloro-4-(3-fluorophenethylamino)pyrimidine-5-carboxylate (1.08 g, 56%). LRMS (M+H+) m/z 323.9.

To a mixture of ester (600 mg, 1.85 mmol), ethanol (5 mL) and THF (5 mL) was added 1N NaOH (5 mL, 5.0 mmol). The reaction mixture was stirred at 50° C. for 1 h. The mixture was concentrated to half volume and adjusted pH to 2-3 with 2N HCl. The precipitate was filtered and washed with water to give the 2-chloro-4-(3-fluorophenethylamino)pyrimidine-5-carboxylic acid in quantitative yield. LRMS (M+H+) m/z 296.0.

A mixture of chloride 2-chloro-4-(3-fluorophenethylamino)pyrimidine-5-carboxylic acid (207 mg, 0.7 mmol), borolane (177 mg, 0.91 mmol), Pd(PPh3)4 (81 mg, 0.07 mmol), K2CO3 (290 mg, 2.1 mmol) and anhydrous DMF (2 mL) was degassed with nitrogen for 10 min. The mixture was then stirred at 130° C. in microwave for 1 h. The mixture was filtered through the Cetite and washed with DMF. The filtrate was adjusted to pH 4 with 2N HCl, and diluted with EtOAc. The organic layer was washed with brine twice and concentrated to dryness. The residue was triturated with dichloromethane (300 mL). Filtration followed by washed with EtOAc gave the desired product 4-(3-fluorophenethylamino)-2-(1H-pyrazol-4-yl)pyrimidine-5-carboxylic acid as a off-white solid (149 mg, 65%). LRMS (M+H+) m/z 328.3.

To a mixture of acid (65 mg, 0.2 mmol) in DMF (2 mL) was added HBTU (95 mg, 0.25 mmol), HOBt (34 mg, 0.25 mmol), then 2-aminomethylpyridine (0.026 mL, 0.25 mmol). The reaction mixture was stirred at room temperature for 1 h. The crude mixture was purified on RP-HPLC using a mixture of acetonitrile and H2O to give 2-(3-fluorophenethylamino)-6-(1H-pyrazol-4-yl)-N-(pyridin-2-ylmethyl)nicotinamide (60 mg, 72%). LRMS (M+H+) m/z 418.1.

Example III Assays

Screening assays were performed using a pyruvate kinase and lactate dehydrogenase-coupled ATPase assay containing the following reagents: Potassium PIPES (50 mM), MgCl2 (3 mM), KCl (100 mM), ATP (0.15 mM), DTT (1 mM), BSA (0.1 mg/ml), NADH (0.5 mM), PEP (1.5 mM), pyruvate kinase (4 U/ml), lactate dehydrogenase (8 U/ml), and antifoam (50 ppm) (concentrations expressed are final assay concentrations). The pH was adjusted to 6.80 at 22° C. by addition of potassium hydroxide. Lead optimization assays were performed with a more sensitive pyruvate kinase/horseradish peroxidase/pyruvate oxidase-coupled ATPase assay containing the following reagents: Potassium PIPES (12 mM), MgCl2 (2 mM), KCl (100 mM), ATP (0.15 mM), BSA (0.05 mg/ml), potassium phosphate (2 mM), amplex red (0.1 mM), PEP (0.1 mM), pyruvate kinase (4 U/ml), horseradish peroxidase (0.5 U/ml), pyruvate oxidase (0.5 U/ml), and antifoam (50 ppm) (concentrations expressed are final assay concentrations). The pH was adjusted to 7.00 at 22° C. by addition of potassium hydroxide.

The protein components specific to this assay are chicken gizzard smooth muscle myosin subfragment-1 that has been chemically crosslinked to either cardiac or skeletal actin using an excess of 1-ethyl-3-[3-dimethylaminopropyl]carbodiimide hydrochloride and N-hydroxysuccinimide. The exact concentration of the crosslinked smooth muscle myosin in the assay is determined empirically, by “titration” to achieve a desired rate of ATP hydrolysis. The concentration varies between protein preparations due to variations in the fraction of active molecules in each preparation.

Compound dose response assays are performed by first preparing a dilution series of test compound, each with an assay mixture containing potassium PIPES, MgCl2, KCl, ATP, BSA, potassium phosphate, amplex red, PEP, crosslinked smooth muscle actomyosin (subfragment-1), antifoam, and water. The assay is started by adding an equal volume of solution containing potassium Pipes, MgCl2, KCl, BSA, potassium phosphate, pyruvate kinase, horseradish peroxidase, pyruvate oxidase, antifoam, and water. ATP hydrolysis is monitored by measuring the fluorescence of amplex red (excitation at 480 nm, emission at 615 nm). The resulting dose response curve is fit by the 4 parameter equation y=Bottom+((Top-Bottom)/(1+((IC50/X)̂Hill))). The IC50 is defined as the concentration at which ATPase activity is midway between the top and bottom of the dose response curve.

Example IV Synthesized Compounds

Using procedures described herein or procedures similar thereto, the compounds in the following table were synthesized and tested.

IC50 m/z Median M + H+ CHEMICAL NAME 18.807 414.1 {2-(3,4-difluorophenyl)-4-[(2-(2- pyridyl)ethyl)amino]pyrimidin-5-yl}- N-(2-methoxyethyl)carboxamide 3.229 460.1 (2-(3,4-difluorophenyl)-4-{[2-(3- methylphenyl)ethyl]amino}pyrimidin-5-yl)-N-(3- pyridylmethyl)carboxamide 1.685 447.1 {2-(3,4-difluorophenyl)-4-[(2-(2- pyridyl)ethyl)amino]pyrimidin-5-yl}- N-(3-pyridylmethyl)carboxamide 24.8 398.1 {2-(3,4-difluorophenyl)-4-[(2-(2- pyridyl)ethyl)amino]pyrimidin-5-yl}- N-(methylethyl)carboxamide 4.016 446.1 {2-(3,4-difluorophenyl)-4-[(2-(2- pyridyl)ethyl)amino]pyrimidin-5-yl}- N-benzylcarboxamide 1.804 447.1 {2-(3,4-difluorophenyl)-4-[(2-(2- pyridyl)ethyl)amino]pyrimidin-5-yl}- N-(4-pyridylmethyl)carboxamide 23.931 427.1 (2-(3,4-difluorophenyl)-4-{[2-(3- methylphenyl)ethyl]amino}pyrimidin-5-yl)-N-(2- methoxyethyl)carboxamide 1.925 460.1 (2-(3,4-difluorophenyl)-4-{[2-(3- methylphenyl)ethyl]amino}pyrimidin-5-yl)-N-(4- pyridylmethyl)carboxamide 2.744 460.1 (2-(3,4-difluorophenyl)-4-{[2-(3- methylphenyl)ethyl]amino}pyrimidin-5-yl)-N-(2- pyridylmethyl)carboxamide 4.73 447.1 {2-(3,4-difluorophenyl)-4-[(2-(2- pyridyl)ethyl)amino]pyrimidin-5-yl}- N-(2-pyridylmethyl)carboxamide 2.743 418.1 (4-{[2-(3-fluorophenyl)ethyl]amino}- 2-pyrazol-4-ylpyrimidin-5-yl)-N- (2-pyridylmethyl)carboxamide 3.078 418.1 (4-{[2-(3-fluorophenyl)ethyl]amino}- 2-pyrazol-4-ylpyrimidin-5-yl)-N- (3-pyridylmethyl)carboxamide

While the present invention has been described with reference to the specific embodiments thereof, it should be understood by those skilled in the art that various changes may be made and equivalents may be substituted without departing from the true spirit and scope of the invention. In addition, many modifications may be made to adapt a particular situation, material, composition of matter, process, process step or steps, to the objective, spirit and scope of the present invention. All such modifications are intended to be within the scope of the claims appended hereto.

Claims

1. At least one chemical entity chosen from compounds of Formula I and pharmaceutically acceptable salts thereof wherein

R1 is selected from hydrogen and optionally substituted alkyl; cyano, halo, azido, optionally substituted amino, optionally substituted alkoxy, optionally substituted aryloxy, optionally substituted alkoxycarbonyl, optionally substituted aminocarbonyl, optionally substituted aminosulfonyl, sulfonyl, sulfinyl, and sulfanyl;
Z1 is selected from optionally substituted aryl, optionally substituted heteroaryl, optionally substituted cycloalkyl, and optionally substituted heterocycloalkyl, cyano, optionally substituted alkyl, optionally substituted acyl, optionally substituted alkoxycarbonyl, optionally substituted amino, optionally substituted aminocarbonyl, optionally substituted aminosulfonyl, optionally substituted carbamimidoyl, optionally substituted alkoxy, optionally substituted aryloxy, optionally substituted heteroaryloxy, optionally substituted heterocycloalkyloxy, optionally substituted alkenyl, optionally substituted alkynyl, sulfonyl, sulfinyl, and sulfanyl;
Z2 is selected from optionally substituted amidino, carboxyl, optionally substituted alkoxy carbonyl, optionally substituted acyl, optionally substituted alkenyl, optionally substituted alkyl, optionally substituted heterocycloalkyl, optionally substituted heteroaryl, and optionally substituted aminocarbonyl;
Z3 is chosen from hydrogen and optionally substituted alkyl; and
R3 is chosen from hydrogen and optionally substituted alkyl.

2. At least one chemical entity of claim 1 wherein Z1 is chosen from heteroaryl and phenyl, each of which is optionally substituted with one, two or three groups chosen from halo, optionally substituted lower alkyl, and optionally substituted lower alkoxy.

3. At least one chemical entity of claim 2 wherein Z1 is chosen from pyrazolyl, phenyl, and phenyl substituted with one, two, or three groups chosen from halo, optionally substituted lower alkyl, and optionally substituted lower alkoxy.

4. At least one chemical entity of claim 3 wherein Z1 is chosen from pyrazolyl, phenyl, and phenyl substituted with one, two, or three halo groups.

5. At least one chemical entity of claim 4 wherein Z1 is chosen from pyrazolyl, phenyl, 3-fluorophenyl, 4-fluorophenyl, and 3,4-difluorophenyl.

6. At least one chemical entity of claim 1 wherein Z2 is aminocarbonyl.

7. At least one chemical entity of claim 6 wherein Z2 is —C(O)—NHR4 wherein R4 is optionally substituted lower alkyl.

8. At least one chemical entity of claim 7 wherein R4 is chosen from lower alkyl optionally substituted with phenyl, pyridyl, and lower alkoxy.

9. At least one chemical entity of claim 8 wherein R4 is chosen from 2-methoxyethyl, benzyl, isopropyl, pyridin-2-ylmethyl, pyridin-3-ylmethyl, and pyridin-4-ylmethyl.

10. At least one chemical entity of claim 1 wherein Z3 is chosen from ethyl, methyl and propyl, each of which is substituted with a group independently selected from optionally substituted aryl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, and optionally substituted heteroaryl.

11. At least one chemical entity of claim 10 wherein Z3 is chosen from 2-(phenyl)ethyl, benzyl, 2-(pyridin-2-yl)ethyl, and pyridin-2-ylmethyl, each of which is optionally substituted.

12. At least one chemical entity of claim 11 wherein Z3 is chosen from 2-(phenyl)ethyl, benzyl, 2-(pyridin-2-yl)ethyl, and pyridin-2-ylmethyl, each of which is optionally substituted with one or two groups chosen from lower alkyl, lower alkoxy, halo, and hydroxy.

13. At least one chemical entity of claim 12 wherein Z3 is chosen from 2-(3-fluorophenyl)ethyl, 2-(3-methylphenyl)ethyl, 2-(pyridin-2-yl)ethyl, 2-(3-methylphenyl)ethyl and pyridin-2-ylmethyl.

14. At least one chemical entity of claim 1 wherein R1 is chosen from hydrogen and optionally substituted lower alkyl.

15. At least one chemical entity of claim 14 wherein R1 is chosen from hydrogen and lower alkyl.

16. At least one chemical entity of claim 15 wherein R1 is chosen from hydrogen and methyl.

17. At least one chemical entity of claim 16 wherein R1 is hydrogen.

18. At least one chemical entity of claim 1 wherein R3 is chosen from hydrogen and optionally substituted lower alkyl.

19. At least one chemical entity of claim 18 wherein R3 is chosen from hydrogen and lower alkyl.

20. At least one chemical entity of claim 19 wherein R3 is chosen from hydrogen and methyl.

21-28. (canceled)

Patent History
Publication number: 20090198057
Type: Application
Filed: Jan 23, 2009
Publication Date: Aug 6, 2009
Inventors: Pu-Ping LU (Foster City, CA), Chihyuan Grace CHUANG (San Mateo, CA), Bradley P. MORGAN (Moraga, CA), David J. MORGANS, JR. (Los Altos, CA)
Application Number: 12/359,177
Classifications
Current U.S. Class: Additional Hetero Ring Which Is Unsaturated (544/328)
International Classification: C07D 401/14 (20060101);